Prediction of Enzyme Classification from Protein Sequence without the Use of Sequence Similarity. - Marie desJardins; Peter D. Karp; Markus Krummenacker; Thomas J. Lee; Christos A. Ouzounis (ISMB, 1997)

Bayesian Network Classification with Continuous Attributes: Getting the Best of Both Discretization and Parametric Fitting. - Nir Friedman; Moisés Goldszmidt; Thomas J. Lee (ICML, 1998)

Generating qualitatively Different Plans througt Metatheoretic Biases. - Karen L. Myers; Thomas J. Lee (AAAI/IAAI, 1999)

Active Coordination of Distributed Human Planners. - Karen L. Myers; Peter Jarvis; Thomas J. Lee (AIPS, 2002)

Interactive Execution Monitoring of Agent Teams. - David E. Wilkins; Thomas J. Lee; Pauline Berry (J. Artif. Intell. Res., 2003)

Online Query Relaxation via Bayesian Causal Structures Discovery. - Ion Muslea; Thomas J. Lee (AAAI, 2005)

BioWarehouse: a bioinformatics database warehouse toolkit. - Thomas J. Lee; Yannick Pouliot; Valerie Wagner; Priyanka Gupta; David W. J. Stringer-Calvert; Jessica D. Tenenbaum; Peter D. Karp (BMC Bioinform., 2006)

BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats. - Peter D. Karp; Thomas J. Lee; Valerie Wagner (DILS, 2008)

Annotation-based inference of transporter function. - Thomas J. Lee; Ian T. Paulsen; Peter D. Karp (ISMB, 2008)

Airlift mission monitoring and dynamic rescheduling. - David E. Wilkins; Stephen F. Smith; Laurence A. Kramer; Thomas J. Lee; Timothy W. Rauenbusch (Eng. Appl. Artif. Intell., 2008)

Iteration Learning by Demonstration. - Steven Eker; Thomas J. Lee; Melinda T. Gervasio (AAAI Spring Symposium: Agents that Learn from Human Teachers, 2009)

Learning by Demonstration to Support Military Planning and Decision Making. - Thomas D. Garvey; Melinda T. Gervasio; Thomas J. Lee; Karen L. Myers; Carl Angiolillo; Matthew E. Gaston; Janette Knittel; Jake Kolojejchick (IAAI, 2009)

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. - Peter D. Karp; Suzanne M. Paley; Markus Krummenacker; Mario Latendresse; Joseph M. Dale; Thomas J. Lee; Pallavi Kaipa; Fred Gilham; Aaron Spaulding; Liviu Popescu; Tomer Altman; Ian T. Paulsen; et al. (Briefings Bioinform., 2010)

How to serve soup: interleaving demonstration and assisted editing to support nonprogrammers. - Melinda T. Gervasio; Will Haines; David N. Morley; Thomas J. Lee; C. Adam Overholtzer; Shahin Saadati; Aaron Spaulding (IUI, 2011)

Discovering action idioms bridging the gap between system-level events and human-level actions. - Melinda T. Gervasio; Thomas J. Lee (VL/HCC, 2013)

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. - Peter D. Karp; Mario Latendresse; Suzanne M. Paley; Markus Krummenacker; Quang Ong; Richard Billington; Anamika Kothari; Daniel S. Weaver; Thomas J. Lee; Pallavi Subhraveti; Aaron Spaulding; Carol A. Fulcher; et al. (Briefings Bioinform., 2016)